Evidence map›Paper›PMID 30975199›Full record

ArticleBMC research notes2019

A human specific Alu DNA cassette is found flanking the genes of transcription factor AP2.

Hamdi K Hamdi, Siddana Reddy, Nada Laz, Renad Eltaher, Zahraa Kandell, Teif Mahmud, Lamia Alenazi, Basheer Haroun, Mohanad Hassan, Raju Ragavendra

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC research notes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.3field-weighted citation impact, top 44% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 5 citations in OpenAlex.

  1. Article
  2. Article
  3. AnNAR genomics and bioinformatics · 2022
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 1 institution in 1 country.

Hamdi K HamdiBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia. 282hamdi@gmail.com.ORCID http://orcid.org/0000-0001-6976-0874
Siddana ReddyBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Nada LazBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Renad EltaherBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Zahraa KandellBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Teif MahmudBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Lamia AlenaziBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Basheer HarounBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Mohanad HassanBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Raju RagavendraBasic Medical Sciences Dept., College of Dentistry, Almustqbal University, PO Box 156, Buraida, Qassim, 51411, Saudi Arabia.
Qassim University · SA

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

objectiveAlu elements are retroposons that invaded the primate genome and shaped its biology. Some Alus inserted recently and are polymorphic in the human population. It is these Alus that are being sought after in disease association studies and regulatory biology. Discovering polymorphic Alus in the human genome can open areas of new research in these fields.

resultsUsing the polymerase chain reaction on genomic DNA, we identified a polymorphic Alu in the flanking region of the TFAP2B and TFAP2D genes. The new insert was found in higher frequency in Europeans (0.4) and Asians (0.38) and lower frequency in Africans (0.25). We also show this Alu to be part of a 3 Alu cassette that is human specific. The TFAP2B and TFAP2D genes encode members of the transcription factor AP-2, which plays a role in organ development. The insertion of this Alu cassette flanking the transcription factor genes distinguishes humans from the primates. This cassette can possibly affect the regulation of both genes or alternately provoke genomic deletions, which we have shown in this study. Its presence in such a location is intriguing and unquestionably opens an investigational window in disease association studies and in the field of gene regulation.

Indexed as

3' Flanking Region5' Flanking RegionAlu ElementsGenome, HumanMutagenesis, InsertionalAsian PeopleBase SequenceBlack PeopleDatabases, Nucleic AcidEndothelial CellsEndothelium, VascularGene ExpressionHumansPolymorphism, GeneticPrimary Cell CultureSequence AlignmentTFAP2B protein, humanTFAP2D protein, humanTranscription Factor AP-2AluAP2Breast cancerDentalNeuralPolymorphicTFAP2BTFAP2D

Identifiers

PMID30975199
PMCPMC6458609
OpenAlexW2944463095

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.