Publications by authors named "Hongjuan He"

42 Publications

Spatiotemporal expression of retrogene-host pair Mcts2/H13 in mouse embryo, and Mcts2 has no influence on H13 transcription pattern in NIH/3T3 cells.

Acta Histochem 2014 Mar 21;116(2):312-8. Epub 2013 Sep 21.

School of Life Science and Biotechnology, State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, No. 92 West Da-zhi Street, Harbin, Heilongjiang 150001, China. Electronic address:

Mcts2 and H13 comprise an imprinted retrogene-host gene pair. Imprinted genes have been proved to be closely related with embryo development. In order to understand its expression relationship during embryo development and influence of the retrogene on the host gene, we studied expression patterns in mouse embryos and transcriptional interference in a cell culture system. The present study determined the spatio-temporal expression pattern of Mcts2 and H13 from embryonic day 9.5 to 15.5. A similar expression pattern between Mcts2 and H13 was observed in mouse embryogenesis by in situ hybridization and real-time PCR, these two genes were extensively expressed in the neural tissues at mid-embryonic stages. As the embryo development proceeded, H13 and Mcts2 were widely detected throughout the developing organism, especially highly expressed in brain. Moreover, neither over expression nor knockdown of Mcts2 has any significant detectable effect on H13 expression in NIH/3T3 cells. In addition, transcriptional up-regulation of Mcts2 caused by demethylation of DMR in the Mcts2 promoter was not directly associated with the H13 transcription in NIH/3T3 cells treated by 5-Aza-cdR. The regulatory relationship between H13 transcripts and the promoter methylation status of Mcts2 was complex, demonstrating host/retrogene relationship may not be limited to the imprinted locus.
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http://dx.doi.org/10.1016/j.acthis.2013.08.008DOI Listing
March 2014

Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features.

Nucleic Acids Res 2013 Dec 13;41(22):10044-61. Epub 2013 Sep 13.

School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China and College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.

In silico prediction of genomic long non-coding RNAs (lncRNAs) is prerequisite to the construction and elucidation of non-coding regulatory network. Chromatin modifications marked by chromatin regulators are important epigenetic features, which can be captured by prevailing high-throughput approaches such as ChIP sequencing. We demonstrate that the accuracy of lncRNA predictions can be greatly improved when incorporating high-throughput chromatin modifications over mouse embryonic stem differentiation toward adult Cerebellum by logistic regression with LASSO regularization. The discriminating features include H3K9me3, H3K27ac, H3K4me1, open reading frames and several repeat elements. Importantly, chromatin information is suggested to be complementary to genomic sequence information, highlighting the importance of an integrated model. Applying integrated model, we obtain a list of putative lncRNAs based on uncharacterized fragments from transcriptome assembly. We demonstrate that the putative lncRNAs have regulatory roles in vicinity of known gene loci by expression and Gene Ontology enrichment analysis. We also show that the lncRNA expression specificity can be efficiently modeled by the chromatin data with same developmental stage. The study not only supports the biological hypothesis that chromatin can regulate expression of tissue-specific or developmental stage-specific lncRNAs but also reveals the discriminating features between lncRNA and coding genes, which would guide further lncRNA identifications and characterizations.
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http://dx.doi.org/10.1093/nar/gkt818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905897PMC
December 2013

Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data.

PLoS One 2013 14;8(8):e71152. Epub 2013 Aug 14.

School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China.

Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071152PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743905PMC
March 2014

miR-370 is stage-specifically expressed during mouse embryonic development and regulates Dnmt3a.

FEBS Lett 2013 Mar 8;587(6):775-81. Epub 2013 Feb 8.

School of Life Science and Biotechnology, Harbin Institute of Technology, No 92 West Da-zhi Street, Harbin, Heilongjian 150001, China.

MicroRNAs (miRNAs) are small non-coding RNAs that participate in a large variety of biological processes. In this paper, the spatiotemporal expression pattern of miR-370 was characterized during mouse embryonic development, and was found to be stage- and tissue-specifically expressed. In addition, through luciferase reporter assays and western blot analyses, DNA methyltransferase 3A (Dnmt3a) was identified as a directly regulated target of miR-370. Altogether, our results indicate that miR-370 may play important roles in the morphogenesis of diverse organs, especially brain and adrenal glands, by mediating Dnmt3a expression during mouse development.
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http://dx.doi.org/10.1016/j.febslet.2013.01.070DOI Listing
March 2013

Expression patterns of ubiquitin conjugating enzyme UbcM2 during mouse embryonic development.

Gene Expr 2012 ;15(4):163-70

School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Heilongjiang, China.

Ubiquitin conjugating enzyme UbcM2 (Ubiquitin-conjugating enzymes from Mice, the number reveals the identification order) has been implicated in many critical processes, such like growth-inhibiting, mediating cell proliferation and regulation of some transcription factor, but the expression profile during mouse embryo development remains unclear. Hereby, during mid-later embryonic stage, the expression patterns of UbcM2 were examined using in situ hybridization and quantitative real-time PCR (qRT-PCR). The signals were significantly intense in central nervous system and skeletal system, weak in tongue, heart, lung, liver, and kidney. In the central nervous system, UbcM2 was principally expressed in thalamus, external germinal layer of cerebellum (EGL), mitral cell layer of olfactory bulb, hippocampus, marginal zone and ventricular zone of cerebral cortex, and spinal cord. In the skeletal system, UbcM2 was primarily expressed in proliferating cartilage. Furthermore, qRT-PCR analysis displayed that the expression of UbcM2 was ubiquitous at E15.5, most prominent in brain, weaker in lung liver and kidney, accompanied by the lowest level in tongue and heart. During brain development, the expression level of UbcM2 first ascended and then decreased from E12.5 to E18.5, the peak of which sustained starting at E14.5 until E16.5. Together, these results suggest that UbcM2 may play potential roles in the development of mouse diverse tissues and organs, particularly in the development of brain and skeleton.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043840PMC
http://dx.doi.org/10.3727/105221612x13372578119616DOI Listing
August 2012

Trmt112 gene expression in mouse embryonic development.

Acta Histochem Cytochem 2012 Apr 14;45(2):113-9. Epub 2012 Mar 14.

School of Life Science and Biotechnology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 92 West Da-zhi Street, Harbin, 150001, Heilongjiang, China.

Mouse Trmt112, the homologous gene of yeast Trm112 (tRNA methyltransferase 11-2), was initially cloned from RIKEN with uncertain function. The yeast TRM112 is now known to play important roles in RNA methylation. Here, we studied the expression of Trmt112 by in situ hybridization and quantitative real-time RT-PCR (QRT-PCR). A higher expression level of Trmt112 was observed in the brain and nervous system by whole mount in situ hybridization from embryonic day 10.5 (E10.5) to E11.5. At later developmental stages E13.5 and E16.5, abundant expression was prominently found in various organs and tissues including developing brain, nervous system, thymus, lung, liver, intestine, kidney, and cartilage. Furthermore, Trmt112 was persistently expressed from E9.5 to E18.5 on whole embryos and highly expressed in multiple organs at E12.5, E15.5 and E18.5 by QRT-PCR. These results showed that Trmt112 gene was highly and ubiquitously expressed during mouse embryonic development, implying that it might be involved in the morphogenesis of diverse organs and tissues and numerous physiological functions.
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http://dx.doi.org/10.1267/ahc.11047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365302PMC
April 2012

A family-based association study of dopamine receptor D4 and mental retardation in Qinba region of China.

Neurosci Lett 2012 May 15;516(1):1-4. Epub 2012 Feb 15.

Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi'an 710069, China.

Dopamine receptor D4 (DRD4) is activated by the neurotransmitter dopamine and links to many neurological and psychiatric conditions because of its close relationship with prefrontal cortex and other important brain regions. To explore the possibility that genetic variants of DRD4 gene predispose to children with mental retardation (MR), five target SNPs of DRD4 were selected and genotyped in the samples of 163 MR pedigrees from the Qinba region of China. Two SNPs (rs752306 and rs3758653) showed weak association with MR (the P values were 0.022 and 0.015 for dominant model, and 0.027 and 0.015 for recessive model, respectively). Although they did not bear the multiple testing corrections, the haplotype which contained rs3758653 exhibited a significant association with MR (global P values were 0.018 for dominant model and 0.028 for recessive model, respectively). The in silico analysis also indicated that rs752306 and rs3758653 would be biologically meaningful SNPs. Therefore, the present study suggested that the genetic variants of DRD4 gene may play an important role in human MR. Further investigations, such as confirmation with other independent samples and functional studies, may elucidate their effect on gene expression and MR susceptibility.
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http://dx.doi.org/10.1016/j.neulet.2012.02.017DOI Listing
May 2012

Expression profile of mouse Mterfd2, a novel component of the mitochondrial transcription termination factor (MTERF) family.

Genes Genet Syst 2011 ;86(4):269-75

State Key Laboratory of Urban Water Resource and Environment, Department of Life Science and Engineering, Harbin Institute of Technology, Heilongjiang, China.

Mterfd2 is a component of mitochondria transcription termination factor (MTERF) family which belongs to the MTERF4 subfamily. In this report, we characterized the expression profile of mouse Mterfd2 during embryogenesis by in situ hybridization (ISH), quantitative real-time PCR (qRT-PCR) and northern blot. The whole mount ISH at E9.5, E10.5 and E11.5 showed that Mterfd2 was dynamically expressed in the brain. Besides, at E9.5 and E10.5 stages, Mterfd2 was persistently expressed in the lateral plate mesoderm and heart; at E10.5 and E11.5 stages, it showed an abundant expression in the limb buds. The tissue ISH of E13.5 and E15.5 suggested that Mterfd2 was ubiquitously expressed, and has the higher expression in the forebrain, diencephalon, midbrain, spinal cord, dorsal root ganglion, tongue, lung, liver and kidney. This ubiquitous expression profile in the late embryogenesis was further confirmed by qRT-PCR and northern blot at E12.5, E15.5 and E18.5 stages. Besides, the results of co-location of EGFP-Mterfd2 fusion protein indicated that Mterfd2 was targeted to the mitochondria. Collectively, these data suggested that Mterfd2 showed a dynamic expression pattern during embryogenesis. It might play an important role in the organ differentiation which was probably resulted from its role in the mitochondrial transcription regulation.
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http://dx.doi.org/10.1266/ggs.86.269DOI Listing
April 2012

Spatiotemporal expression pattern of Mirg, an imprinted non-coding gene, during mouse embryogenesis.

J Mol Histol 2012 Feb 29;43(1):1-8. Epub 2011 Oct 29.

Department of Life Science and Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No.92 West Da-zhi Street, Harbin, Heilongjiang, China.

Recent research has revealed that the maternal non-coding RNA genes (Gtl2, Rian and Mirg) from the Dlk1-Dio3 imprinted cluster are closely related to the full development potential of the induced pluripotent stem cells (iPSCs). Transcriptional silencing of these genes failed to generate all-iPSC mice, indicating their significant contribution to embryogenesis. However, except for Gtl2, little information regarding these genes has been acquired in this cluster. In the present study, we analyzed the spatiotemporal expression patterns of Mirg during mouse embryogenesis. Using in situ hybridization and quantitative PCR, we demonstrated that Mirg non-coding RNA exhibited sustained expression throughout mouse embryogenesis from E8.5 to E18.5. Strong expression was detected in the central nervous system (E9.5-E15.5) and various skeletal muscles (E13.5 and E15.5), and the subcellular localization appeared to be in the nuclei. The pituitary and adrenal gland also showed high expression of Mirg, but, unlike the skeletal muscles and the neural circuitry, the signals were not concentrated in the nuclei. In the major internal organs, Mirg maintained low expression during embryogenesis (E12.5-E18.5) whereas in the liver and the developing lung, Mirg was expressed with a gradually decreasing trend and a gradually raising trend, respectively. These findings indicate that temporal regulation of Mirg expression may be required during specific stages and in specific tissues during embryonic development.
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http://dx.doi.org/10.1007/s10735-011-9367-xDOI Listing
February 2012

Expression of macro non-coding RNAs Meg8 and Irm in mouse embryonic development.

Acta Histochem 2012 Jul;114(4):392-9

State Key Laboratory of Urban Water Resource and Environment, Department of Life Science and Engineering, Harbin Institute of Technology, Heilongjiang, China.

Non-coding RNAs (ncRNAs) Meg8 and Irm were previously identified as alternatively splicing isoforms of Rian gene. Ascertaining ncRNAs spatiotemporal expression patterns is crucial for understanding the physiological roles of ncRNAs during tissue and organ development. In this study in mouse embryos, we focused on the developmental regulation expression of imprinted macro ncRNAs, Meg8 and Irm by using in situ hybridization and quantitative real-time RT-PCR (QRT-PCR). The in situ hybridization results showed that Meg8 and Irm were expressed in the developing brain at embryonic day 10.5 (E10.5) and E11.5, while Irm expression signals were strikingly detected in the somite, where Meg8 expression signals were undetectable. By E15.5, they were expressed in brain, tongue, liver, lung and neuroendocrine tissues, while Irm displayed more restricted expression in tongue and skeletal muscle than Meg8. Furthermore, quantitative analysis confirmed that they were highly expressed in tongue and brain at E12.5, E15.5 and E18.5. These results indicated that Meg8 and Irm might be coordinately expressed and functionally correlated in diverse of organs. Notably, Irm was more closely associated with morphogenesis of skeletal muscle in contrast to Meg8 during embryonic development.
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http://dx.doi.org/10.1016/j.acthis.2011.07.009DOI Listing
July 2012

Expression patterns of imprinted gene Inpp5f-v3 during mouse brain development.

J Mol Histol 2011 Apr 20;42(2):167-73. Epub 2011 Mar 20.

Department of Life Science and Engineering, Harbin Institute of Technology, No. 92 West Da-zhi Street, Harbin, 150001, Heilongjian, China.

Inpp5f-v3 is a transcriptional variant of Inpp5f (inositol polyphosphate-5-phosphatase F) and locates in distal mouse chromosome 7. It is a paternally expressed imprinted gene in mouse. In this study, we examined the spatiotemporal patterns of Inpp5f-v3 gene during the mouse development. The northern blotting analysis revealed that only one transcript approx 2.7 kb of Inpp5f-v3 was detected in brain. The signals were only observed in brain by the whole-mount in situ hybridization at embryonic day 11.5 (E11.5). The results of quantitative real-time PCR (QRT-PCR) showed that the expression of Inpp5f-v3 increased gradually from the E11.5 to E17.5 and reached the highest at E17.5, then decreased at E18.5 during the brain development. Inpp5f-v3 gene was strongly expressed in the cerebral cortex, olfactory bulb, external germinal layer of cerebellum and ventricular zone (Vz) during the embryonic development (E15.5-E19.5), whereas the expression increased in the olfactory bulb and the cerebellum after birth by using in situ hybridization. The results also demonstrated that the expression of Inpp5f-v3 gene mainly located in olfactory bulb and hippocampus at postnatal day 7 (P7) and adulthood. These results suggest that Inpp5f-v3 is specifically expressed in mouse brain, and may function in the development of mouse brain.
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http://dx.doi.org/10.1007/s10735-011-9321-yDOI Listing
April 2011

Expression of non-coding RNA AB063319 derived from Rian gene during mouse development.

J Mol Histol 2011 Apr 9;42(2):105-12. Epub 2011 Feb 9.

State Key Laboratory of Urban Water Resource and Environment, Department of Life Science and Engineering, Harbin Institute of Technology, No. 92 West Da-zhi Street, 150001, Harbin, Heilongjiang, China.

The regulatory functions of many non-coding RNAs (ncRNAs) were widely recognized. However, there are very few publications on long intronic ncRNAs. The transcriptional hierarchy driving a large amount of long and short ncRNAs originated from the maternal chromosome is not clarified in the Dlk1-Dio3 imprinted clusters of mouse distal chromosome 12. Here, we only focused on the previously identified long ncRNA AB063319 which derives from the large imprinted gene Rian and contains three retained introns of Rian, and tried to unsderstand this ncRNAs part of biological functions. We used in situ hybridization and quantitative real-time RT-PCR (QRT-PCR) to characterize the spatiotemporal expression pattern of AB063319 during mouse development. The in situ hybridization results showed that AB063319 was prominently expressed in the brain at embryonic day 10.5 (E10.5) and E11.5, and abundantly expressed in brain, muscle, liver, lung and neuroendocrine tissues at E15.5. Furthermore, quantitative analyses results showed that AB063319 was gradually up-regulated from E9.5 to E18.5 and down-regulated at E19.5 during the mouse embryonic development, and AB063319 was highly expressed in tongue and brain at E12.5, E15.5 and E18.5. Alternatively, AB063319 expression was also predominantly detected in tongue and brain at mouse postnatal day 6 (P6) by semi-quantitative RT-PCR. These results indicated that AB063319, as a stable transcriptional ncRNA, might play the important roles in the morphogenesis of diverse organs and tissues, especially associated with brain and muscle development at mouse embryonic and postnatal stages.
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http://dx.doi.org/10.1007/s10735-011-9312-zDOI Listing
April 2011
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