Combined Analysis of MicroRNome and 3′-UTRome Reveals a Species-specific Regulation of Progesterone Receptor Expression in the Endometrium of Rhesus Monkey

Liu, Ji‐Long; Liang, Xiao-Huan; Su, Ren-Wei; Wei, Lei; Jia, Bo; Feng, Xuemei; Li, Zhixiong; Yang, Zeng‐Ming

doi:10.1074/jbc.m111.301275

Cited by 32 publications

(29 citation statements)

References 54 publications

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“…After trimming and removing the contaminated sequences, 4 936 038 and 4 665 539 clean reads remained (Table ). To consider the robustness of subsequently data analyses, only unique mapping tags (the tags mapped a single locus in the reference genome, called unambiguous clean tags) stayed in the two libraries and were used for further analysis (Liu et al , Shen et al ).…”

Section: Resultsmentioning

confidence: 99%

Genome expression profile analysis reveals important transcripts in maize roots responding to the stress of heavy metal Pb

Shen

Zhang

Chen

et al. 2012

Physiologia Plantarum

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Lead (Pb) has become one of the most abundant heavy metal pollutants of the environment. With its large biomass, maize could be an important object for studying the phytoremediation of Pb-contaminated soil. In our previous research, we screened 19 inbred lines of maize for Pb concentration, and line 178 was identified to be a hyperaccumulator for Pb in both the roots and aboveground parts. To identify important genes and metabolic pathways related to Pb accumulation and tolerance, line 178 was underwent genome expression profile under Pb stress and a control (CK). A total of approximately 11 million cDNA tags were sequenced and 4 665 539 and 4 936 038 clean tags were obtained from the libraries of the test and CK, respectively. In comparison to CK, 2379 and 1832 genes were identified up- or downregulated, respectively, more than fivefolds under Pb stress. Interestingly, all the genes were related to cellular processes and signaling, information storage and processing or metabolism functions. Particularly, the genes involved in posttranslational modification, protein turnover and chaperones; signal transduction, carbohydrate transport and metabolism; and lipid transport and metabolism significantly changed under the treatment. In addition, seven pathways including ribosome, photosynthesis, and carbon fixation were affected significantly, with 118, 12, 34, 21, 18, 72 and 43 differentially expressed genes involved. The significant upregulation of the ribosome pathway may reveal an important secret for Pb tolerance of line 178. And the sharp increase of laccase transcripts and metal ion transporters were suggested to account in part for Pb hyperaccumulation in the line.

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Section: Resultsmentioning

confidence: 99%

Genome expression profile analysis reveals important transcripts in maize roots responding to the stress of heavy metal Pb

Shen

Zhang

Chen

et al. 2012

Physiologia Plantarum

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“…This appears to be logical because microRNAs target numerous mRNAs, it is estimated up to hundreds, and a change in the microRNA sequence is much more dramatic from an evolutionary point of view than a step-by-step modification of the target sequences, which in each case only affects one gene. Examples of such nonconserved targets are known for the progesterone receptor (PGR) in the endometrium of the rhesus monkey (Liu et al, 2012): while miR-96 targets the mRNA of this receptor in human and rhesus monkey it does not in the mouse and rat (Fig. 1).…”

Section: Chromosome 19 Microrna Clustermentioning

confidence: 98%

“…1). The regulation of PGR through miR-375 is specific exclusively to the rhesus monkey and miR-219-5p regulates PGR via a primate-specific long noncoding RNA (Liu et al, 2012).…”

Section: Chromosome 19 Microrna Clustermentioning

confidence: 99%

Only humans have human placentas: molecular differences between mice and humans

Schmidt¹,

Morales-Prieto²,

Pastuschek³

et al. 2015

Journal of Reproductive Immunology

183

117

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“…To assess whether our observation of contaminant sRNAs was also pertinent in other sequencing datasets of low-input samples, the levels of confirmed contaminant sRNA sequences in published datasets (17,18,29,(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)(56)(57)(58)(59)(60)(61) were assessed. Irrespective of the RNA isolation procedure applied, nontarget sequences were detected (making up between 5 and over 99 % of the sequencing libraries for the human samples; Supplementary Table 1).…”

Section: Detection Of Contaminant Sequences In Public Datasetsmentioning

confidence: 99%

Isolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants

Heintz‐Buschart

Yusuf

Kaysen

et al. 2017

Preprint

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Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments.Due to its inherent instability, contamination with RNA is usually considered to be unlikely. Here we report the presence of small RNA (sRNA) contaminants in widely used microRNA extraction kits and means for their depletion. Sequencing of sRNAs extracted from human plasma samples was performed and significant levels of non-human (exogenous) sequences were detected. The source of the most abundant of these sequences could be traced to the microRNA extraction columns by qPCRbased analysis of laboratory reagents. The presence of artefactual sequences originating from the confirmed contaminants were furthermore replicated in a range of published datasets. To avoid artefacts in future experiments, several protocols for the removal of the contaminants were elaborated, minimal amounts of starting material for artefact-free analyses were defined, and the reduction of contaminant levels for identification of bona fide sequences using 'ultra-clean' extraction kits was confirmed. In conclusion, this is the first report of the presence of RNA molecules as contaminants in laboratory reagents. The described protocols should be applied in the future to avoid confounding sRNA studies.

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Combined Analysis of MicroRNome and 3′-UTRome Reveals a Species-specific Regulation of Progesterone Receptor Expression in the Endometrium of Rhesus Monkey

Cited by 32 publications

References 54 publications

Genome expression profile analysis reveals important transcripts in maize roots responding to the stress of heavy metal Pb

Genome expression profile analysis reveals important transcripts in maize roots responding to the stress of heavy metal Pb

Only humans have human placentas: molecular differences between mice and humans

Isolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants

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