NONHSAT102417

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Annotated Information

Name

DHFR upstream transcripts

Characteristics

DHFR upstream transcripts initiate from an upstream minor promoter of the DHFR (dihydrofolate reductase) gene and extend from approximately 400 nucleotide upstream of the 5'-untranslated region of DHFR (which corresponds to DHFR major/core promoter), to the second intron of the DHFR gene where they terminate (Masters (1985), Martianov (2007)). Therefore, the region located between minor and major transcript initiation sites (~400 bp) corresponds to a noncoding transcript and is a promoter of DHFR.

Discrete DHRF upstream initiating transcripts of diverse sizes have been reported, including five major discrete species with sizes of 4.3, 3.8, 3.1, 2.1, and 1.0 kb and four minor ones with sizes of 7.3, 5.0, 1.4, and 0.8kb. Primarily in the poly(A)+ fraction (Masters (1985)). DHFR upstream transcripts adopt a series of structures in vitro that are dependent on the G-tract encompassed in its sequence (Blume (2003)).

Transcriptomic Nomeclature

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Function

Initial studies indicated that DHFR upstream transcripts could impair the formation of the preinitiation complex (PIC) on the major promoter in vitro, thereby repressing the transcriptional activity of the major DHFR promoter (Blume (2003)). DHFR upstream transcripts were shown to inhibit transcription from the DHFR core promoter in-trans in a concentration-dependent manner in in-vitro runoff transcription assays. Transcription factor binding sites positioned between the minor and major promoters within the DHFR gene were indicated to be affected by the upstream regulatory transcripts, which selectively sequestered transcription factor Sp3, and to a lesser extent Sp1, preventing their binding to the DHRF core promoter. The sequestration of Sp3 and Sp1 by the DHFR upstream transcripts appears to involve an altered conformation of the RNA, and a structural domain of the protein distinct from that required for binding DNA (Blume (2003)). However, in-vitro experiments confirmed that transcription from the major promoter could be suppressed in-trans in the absence of Sp1 or any other upstream activating sequence (Akoulitchev (1995), Martianov (2007)).

A more recent study demonstrated that these promoter associated transcripts act as interfering transcripts, directly interacting with TFIIB and dissociate the PIC efficiently to repress DHFR expression (Martianov (2007)). Transcription of the regulatory RNA in trans has a repressive effect on the major DHFR promoter only when the transcript contained the sequence of the core major DHFR promoter (Martianov (2007)). In addition, the major DHFR promoter is GC-rich and contains several G-track sequences (Blume (2003)), and specific and stable triplex structures have been shown to form between the DHFR upstream transcripts and the major promoter, which may contribute to promoter targeting and repression in vivo (Martianov (2007)) (Blume (2003)).

A comparison of in-vitro transcription from templates containing DHFR minor, major or both promoters in their original sequential order indicated very low transcriptional activity when the minor promoter preceded the major one, but robust transcription from the major promoter, suggesting that transcriptional interference in-cis may also play a role in DHFR inhibition by DHFR upstream transcripts (Martianov (2007)).

Regulation

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Expression

Enriched in the nucleus (Masters (1985)).

At least six minor 5' ends mapping upstream of the DHFR gene correspond to approximately 1% of the DHFR-specific polysomal polyA RNA. Most of these species have been found in 6A3 cells, VA2-B cells (the parental line of 6A3), and in HeLa cells (Masters (1985)).

DHFR upstream transcripts accumulate in a population of serum-starved, contact-inhibited (quiescent) U2OS cells, in which the levels of DHFR mRNA are markedly reduced (Martianov (2007)).

Misc

Unpublished analysis of the epigenetic effects of DHFR upstream transcripts indicated similarities to epigenetic markers associated with transcriptional gene silencing induced by the targeted application of synthetic antigene RNAs complementary to the promoter regions of mammalian genes (Martianov (2007)).

DHFR is the major target of methotrexate, a key component in childhood acute lymphoblastic leukemia (ALL) treatment. DNA variations of major promoter/noncoding transcript region and specifc haplotype subtypes involving this region have been associated with childhood ALL, including associations with high-risk patients and lower event-free survival. One particular haplotype (Haplotype *1b) is associated with higher DHFR expression (Al-Shakfa (2009)).

Allelic Information and Variation

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Evolution

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Labs working on this lncRNA

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References

Annotation originally sourced from lncRNAdb.

Basic Information

Transcript ID	NONHSAT102417
Source	NONCODE4.0
Same with	,
Classification	antisense,sense
Length	587 nt
Genomic location	chr5+:79950179..79950765
Exon number	1
Exons	79950179..79950765
Genome context
Sequence	000001 AGCCTGCGCC CGTTTGGGTC CCATCGCCCC GGCCCGGCAG ATACCTGAGC GGTGGCCAGG GCAGGTCCCC GTTCTTGCCG 000080 000081 ATGCCCATGT TCTGGGACAC AGCGACGATG CAGTTTAGCG AACCAACCAT GACAGCAGCG GGAGGACCTC CGAGCCCGCT 000160 000161 CGTTACAGCA GAACGCGCGG TCAAGTTTGG CGCGAAATTG TGGCCGCCCC GCCCCCCTCG TCCCCATTTG TGCAGGCGAG 000240 000241 GCCCCGCCCC CCCGCCCCGG CGCACGCAGG GTCGCGGCGT GCTCGCGCCC GCAGACGCCT GGGAACTGCG GCCGCGGGCT 000320 000321 CGCGCTCCTC GCCAGGCCCT GCCGCCGGGC TGCCATCCTT GCCCTGCCAT GTCTCGCCGG AAGCCTGCGT CGGGCGGCCT 000400 000401 CGCTGCCTCC AGCTCAGCCC CTGCGAGGCA AGCGGTTTTG AGCCGATTCT TCCAGTCTAC GGGAAGCCTG AAATCCACCT 000480 000481 CCTCCTCCAC AGGTGCAGCC GACCAGGTGG ACCCTGGCGC TGCAGCGGCT GCAGCGGCCG CAGCGGCCGC AGCGCCCCCA 000560 000561 GCGCCCCCAG CTCCCGCCTT CCCGCCC

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