Cis-regulation of microRNA expression by scaffold/matrix-attachment regions
Authors: Sreenivas Chavali
Keiko Funa
Pavithra Lakshminarasimhan Chavali
Journal: Nucleic Acids Research (2011)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: miRNAs; gene expression; cis-regulatory elements; scaffold/matrix-attachment regions (MARs); cell type-specific expression
Affiliations: Institute of Biomedicine, Cancer Center Sahlgrenska, University of Gothenburg, Medicinaregatan, Sweden.

Abstract:  microRNAs (miRNAs) spatio-temporally modulate gene expression; however, very little is known about the regulation of their expression. Here, we hypothesized that the well-known cis-regulatory elements of gene expression, scaffold/matrix-attachment regions (MARs) could modulate miRNA expression. Accordingly, we found MARs to be enriched in the upstream regions of miRNA genes. To determine their role in cell type-specific expression of miRNAs, we examined four individual miRNAs (let-7b, miR-17, miR-93 and miR-221) and the miR-17-92 cluster, known to be overexpressed in neuroblastoma. Our results show that MARs indeed define the cell-specific expression of these miRNAs by tethering the chromatin to nuclear matrix. This is brought about by cell type-specific binding of HMG I/Y protein to MARs that then promotes the local acetylation of histones, serving as boundary elements for gene activation. The binding, chromatin tethering and gene activation by HMG I/Y was not observed in fibroblast control cells but were restricted to neuroblastoma cells. This study implies that the association of MAR binding proteins to MARs could dictate the tissue/context specific regulation of miRNA genes by serving as a boundary element signaling the transcriptional activation. 

Retracted: No

PubPeer comments:
 This paper is one of a set of at least 14 papers by the same research group that all appear to share the same photo. In all papers, this photo is used as a zoomed-in inset representing the high-resolution transmission electron microscopy (HRTEM) analysis of the  atomic lattice fringe and particle size of the nanoparticles. Of concern, the same photo, which I have called  Inset 2 , is used to represent a different type of nanoparticle in each of these papers. Here is a collage of 6 different uses of  Inset 2 : ![file] Here is a list of the 14 papers identified so far that all use this photo, and the different types of nanoparticles that they represent. * Betuu0308l Celik et al. - DOI: 10.1016 j.ijhydene.2015.12.138 - Pt(0) DOA@CNT * Betuu0308l Su0327en et al. - DOI: 10.1016 j.ijhydene.2017.05.115 - PdeNi@PEDOT * Betuu0308l Su0327en et al. - DOI: 10.1016 j.ijhydene.2017.06.032 - RuCo@G-MWCNT * Betuu0308l Su0327en et al. - DOI: 10.1016 j.ijhydene.2017.04.213 - RuPtNi@GO * Betuu0308l Su0327en et al. - DOI: 10.1016 j.ijhydene.2017.05.113 - PdNi@GO * Betuu0308l Su0327en et al. - DOI: 10.1016 j.ijhydene.2017.05.112 - Pt@PANI-rGO * Betuu0308l Su0327en et al. - DOI: 10.1016 j.jcis.2018.03.004 - PtNPs@CBH * Betuu0308l Su0327en et al. - DOI: 10.1016 j.jcis.2019.03.057 - PdRu@PVP * Betuu0308l Su0327en et al. - DOI: 10.1016 B978-0-08-102509-3.00002-X - Pd-Ni@AC * Birguu0308tay Su0327ahin et al. - DOI: 10.1016 j.jbiotec.2017.09.012 - Pomegranate Ag NPs * Enes Demir et al. - DOI: 10.1016 j.nanoso.2017.08.018 - Mw-Pt NPs@GO * Enes Demir et al. - DOI: 10.1016 j.nanoso.2017.06.003 - Pt@f-MWCNT * Suleyman Akocak et al. - DOI: 10.1016 j.nanoso.2017.06.002 - Pd@GO * Yagmur Koskun et al. - DOI: 10.1016 j.aca.2018.01.035 - Ni-Pd@AC Of note, this is a different set of papers than the 30 papers by the same group that all appear to use another HRTEM image called  Inset 1 . For an example of that photo and the list of those 30 papers, see DOI 10.1016 j.ijhydene.2018.03.175 https: pubpeer.com publications 8AD71F4A32472314CCE9983D47E36F Here is Figure 2 from this paper, showing the  Inset 2 photo. ![file] , 
 XRD patterns for Pd@GO and Pt@GO in another paper https: pubpeer.com publications 77A598972CEB2B4EE550B813108BB9 are unexpectedly similar: ![file] , 
 Unexpected similarity between Ru XPS spectra of this paper and at least 3 other papers each presenting different material: https: pubpeer.com publications 093160C6A6C6B248F56D44FAA644D9#5 ![file] Also: https: pubpeer.com publications F5517C2786C02B2C34E63266AC642A and https: pubpeer.com publications B0E63DC7297A3FC911A52B3DF7BE37 ,