The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4

Ranzani, Valeria; Rossetti, Grazisa; Panzeri, Ilaria; Arrigoni, Alberto; Bonnal, Raoul Jean Pierre; Curti, Serena Maria; Gruarin, Paola; Provasi, Elena; Sugliano, Elisa; Marconi, Maurizio; Francesco, Raffaele De; Geginat, Jens; Bodega, Beatrice; Abrignani, Sergio; Pagani, Massimiliano

doi:10.1038/ni.3093

Cited by 301 publications

(280 citation statements)

References 53 publications

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“…Distance of lncRNA TSS to FANTOM CAGE peak (log10(bp)) Previous studies in the T-cell lineage had shown that intergenic lncRNA expression is highly restricted even between closely related T-cell subsets. 17 For personal use only. For personal use only.…”

Section: Chromatin Signatures Identify Intergenic Lncrnas With Enhancmentioning

confidence: 98%

“…This is a consequence of the expression patterns of lncRNAs, which are often restricted to 1 or very few tissues or cell types. 9 Recent studies have addressed this limitation by surveying lncRNA expression in several organisms and tissues, [13][14][15][16][17] including murine T cells 18 ; however, there have been no comparable attempts to use sequencing technologies to describe the murine B-cell lncRNA repertoire.…”

Section: Introductionmentioning

confidence: 99%

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Long noncoding RNAs in B-cell development and activation

Brazão

Johnson

Müller

et al. 2016

Blood

106

102

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Long noncoding RNAs (lncRNAs) are potentially important regulators of cell differentiation and development, but little is known about their roles in B lymphocytes. Using RNA-seq and de novo transcript assembly, we identified 4516 lncRNAs expressed in 11 stages of B-cell development and activation. Most of these lncRNAs have not been previously detected, even in the closely related T-cell lineage. Comparison with lncRNAs previously described in human B cells identified 185 mouse lncRNAs that have human orthologs. Using chromatin immunoprecipitation-seq, we classified 20% of the lncRNAs as either enhancer-associated (eRNA) or promoter-associated RNAs. We identified 126 eRNAs whose expression closely correlated with the nearest coding gene, thereby indicating the likely location of numerous enhancers active in the B-cell lineage. Furthermore, using this catalog of newly discovered lncRNAs, we show that PAX5, a transcription factor required to specify the B-cell lineage, bound to and regulated the expression of 109 lncRNAs in pro-B and mature B cells and 184 lncRNAs in acute lymphoblastic leukemia.

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Section: Chromatin Signatures Identify Intergenic Lncrnas With Enhancmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Long noncoding RNAs in B-cell development and activation

Brazão

Johnson

Müller

et al. 2016

Blood

106

102

View full text Add to dashboard Cite

show abstract

“…MAF plays multiple roles in regulation of cellular development and differentiation[65]. Moreover, interaction between long intergenic non-coding RNAs (lincRNAs, linc-MAF-4) and MAF involves in the T lymphocyte differentiation[66]. In addition, an lncRNA-MAF transcription factor network plays an essential role in epidermal differentiation[67].…”

Section: Discussionmentioning

confidence: 99%

Deep sequencing of the mouse lung transcriptome reveals distinct long non-coding RNAs expression associated with the high virulence of H5N1 avian influenza virus in mice

Hu¹,

Hu²,

Wang³

et al. 2018

Virulence

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Long non-coding RNAs (lncRNAs) play multiple key regulatory roles in various biological processes. However, their function in influenza A virus (IAV) pathogenicity remains largely unexplored. Here, using next generation sequencing, we systemically compared the whole-transcriptome response of the mouse lung infected with either the highly pathogenic (A/Chicken/Jiangsu/k0402/2010, CK10) or the nonpathogenic (A/Goose/Jiangsu/k0403/2010, GS10) H5N1 virus. A total of 126 significantly differentially expressed (SDE) lncRNAs from three replicates were identified to be associated with the high virulence of CK10, whereas 94 SDE lncRNAs were related with GS10. Functional category analysis suggested that the SDE lncRNAs-coexpressed mRNAs regulated by CK10 were highly related with aberrant and uncontrolled inflammatory responses. Further canonical pathway analysis also confirmed that these targets were highly enriched for inflammatory-related pathways. Moreover, 9 lncRNAs and 17 lncRNAs-coexpressed mRNAs associated with a large number of targeted genes were successfully verified by qRT-PCR. One targeted lncRNA (NONMMUT011061) that was markedly activated and correlated with a great number of mRNAs was selected for further in-depth analysis, including predication of transcription factors, potential interacting proteins, genomic location, coding ability and construction of the secondary structure. More importantly, NONMMUT011061 was also distinctively stimulated during the highly pathogenic H5N8 virus infection in mice, suggesting a potential universal role of NONMMUT011061 in the pathogenesis of different H5 IAV. Altogether, these results provide a subset of lncRNAs that might play important roles in the pathogenesis of influenza virus and add the lncRNAs to the vast repertoire of host factors utilized by IAV for infection and persistence.

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“…MAF кодирует транскрипционный фактор, вовлеченный в дифференцировку Th2-клеток, а также превраще-ние мезенхимальных стволовых клеток в остеобласты или адипоциты [13]. MAF также требуется для эффектив-ного развития Th17 клеток [14]. MAF входит в подкласс bZIP факторов с основным доменом типа «лейцино-вая застежка».…”

Section: Discussionunclassified

Association of obesity susceptibility gene variants with metabolic syndrome in women

et al. 2017

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Aim. The aim of the study was a replicative analysis of the association of polymorphic variants of genes associated with obesity revealed by results of wide-genomic studies (GWAS) with the development of a cluster of metabolic syndrome risk parameters in women of Bashkir and Tatar ethnicity. The polymorphic markers of the following genes were analyzed: SEC16B, FADS1, KCTD15, MAF, MAP2K5, NEGR1, BDNF, TMEM18. Materials and methods. The study involved 243 women with metabolic syndrome and 298 women without the metabolic syndrome. Amplification of DNA fragments was performed using real-time PCR and TaqMan technique. Results. We found the association the metabolic syndrome with genetic markers of genes MAF and TMEM18 from Tatar. Protective informative marker of the metabolic syndrome among Tatar and Bashkir was the TT haplotype TMEM18 gene (rs2860323 and rs6548238) (р=0.005 and р=0.001, respectively). We identified the association marker rs2241423 MAP2K5 gene with the level of waist circumference (p=0.003) and with the level of cholesterol (p=0.014), the marker rs11084753 KCTD15 gene with glucose levels after exercise (p=0.002), the level of triglycerides (p=0.003) and HDL (p=0.0008) among Tatar women. We identified the association rs2241423 MAP2K5 gene marker to glycated hemoglobin level (p=0.002) and a marker gene rs174550 FADS1 with triglyceride levels (p=0.02) among Bashkir women. Conclusion. It can be assumed that the polymorphic variants FADS1, KCTD15, MAF, MAP2K5, TMEM18 genes are an important part of the genetic structure of predisposition to metabolic syndrome and/or to a cluster of clinical and biochemical indicators of the risk of metabolic syndrome.

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The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4

Cited by 301 publications

References 53 publications

Long noncoding RNAs in B-cell development and activation

Long noncoding RNAs in B-cell development and activation

Deep sequencing of the mouse lung transcriptome reveals distinct long non-coding RNAs expression associated with the high virulence of H5N1 avian influenza virus in mice

Association of obesity susceptibility gene variants with metabolic syndrome in women

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