The BIG Data Center: from deposition to integration to translation

,

doi:10.1093/nar/gkw1060

Cited by 464 publications

(52 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive 70 in BIG Data Center 71 , Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number PRJCA000315 that are publicly accessible at http://bigd.big.ac.cn/gsa , and also deposited in the Gene Expression Omnibus (GEO) under the accession number: GSE93751.…”

Section: Methodsmentioning

confidence: 99%

5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader

et al. 2017

View full text Add to dashboard Cite

5-methylcytosine (m5C) is a post-transcriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. However, its regulatory role in mRNA metabolism is still largely unknown. Here, we reveal that m5C modiﬁcation is enriched in CG-rich regions and in regions immediately downstream of translation initiation sites and has conserved, tissue-specific and dynamic features across mammalian transcriptomes. Moreover, m5C formation in mRNAs is mainly catalyzed by the RNA methyltransferase NSUN2, and m5C is specifically recognized by the mRNA export adaptor ALYREF as shown by in vitro and in vivo studies. NSUN2 modulates ALYREF's nuclear-cytoplasmic shuttling, RNA-binding affinity and associated mRNA export. Dysregulation of ALYREF-mediated mRNA export upon NSUN2 depletion could be restored by reconstitution of wild-type but not methyltransferase-defective NSUN2. Our study provides comprehensive m5C profiles of mammalian transcriptomes and suggests an essential role for m5C modification in mRNA export and post-transcriptional regulation.

show abstract

Section: Methodsmentioning

confidence: 99%

5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader

et al. 2017

View full text Add to dashboard Cite

show abstract

“…The sequence data reported in this paper have been deposited in the Genome Sequence Archive [ 46 ] ( http://bigd.big.ac.cn/gsa/ ) in BIG Data Center [ 47 ], Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number CRA000296. The data supporting the findings of this study are available from the corresponding authors upon request.…”

Section: Methodsmentioning

confidence: 99%

TMCO1 is essential for ovarian follicle development by regulating ER Ca2+ store of granulosa cells

et al. 2018

View full text Add to dashboard Cite

TMCO1 (transmembrane and coiled-coil domains 1) is an endoplasmic reticulum (ER) transmembrane protein that actively prevents Ca2+ stores from overfilling. To characterize its physiological function(s), we generated Tmco1−/− knockout (KO) mice. In addition to the main clinical features of human cerebrofaciothoracic (CFT) dysplasia spectrum, Tmco1−/− females manifest gradual loss of ovarian follicles, impaired ovarian follicle development, and subfertility with a phenotype analogous to the premature ovarian failure (POF) in women. In line with the role of TMCO1 as a Ca2+ load-activated Ca2+ channel, we have detected a supernormal Ca2+ signaling in Tmco1−/− granulosa cells (GCs). Interestingly, although spontaneous Ca2+ oscillation pattern was altered, ER Ca2+ stores of germinal vesicle (GV) stage oocytes and metaphase II (MII) arrested eggs were normal upon Tmco1 ablation. Combined with RNA-sequencing analysis, we also detected increased ER stress-mediated apoptosis and enhanced reactive oxygen species (ROS) level in Tmco1−/− GCs, indicating the dysfunctions of GCs upon TMCO1 deficiency. Taken together, these results reveal that TMCO1 is essential for ovarian follicle development and female fertility by maintaining ER Ca2+ homeostasis of GCs, disruption of which causes ER stress-mediated apoptosis and increased cellular ROS level in GCs and thus leads to impaired ovarian follicle development.

show abstract

“…The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Wang et al, 2017 ) in BIG Data Center Members ( 2017 ), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession numbers CRA000315 that are publicly accessible at http://bigd.big.ac.cn/gsa .…”

Section: Data Availability Statementmentioning

confidence: 99%

Splenic microRNA Expression Profiles and Integration Analyses Involved in Host Responses to Salmonella enteritidis Infection in Chickens

Fan

Wang

et al. 2017

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

To understand the role of miRNAs in regulating genes involved in the host response to Salmonella enteritidis (SE) infection, next generation sequencing was applied to explore the altered splenic expression of microRNAs (miRNAs) and deregulated genes in specific-pathogen-free chickens. Birds were either infected or not (controls, C) and those challenged with SE were evaluated 24 h later and separated into two groups on the basis of the severity of clinical symptoms and blood load of SE: resistant (R, SE challenged-slight clinical symptoms and <105 cfu / 10 μL), and susceptible (S, SE challenged-severe clinical symptoms and >107 cfu/10 μL). Thirty-two differentially expressed (DE) miRNAs were identified in spleen, including 16 miRNAs between S and C, 13 between R and C, and 13 between S and R. Through integration analysis of DE miRNAs and mRNA, a total of 273 miRNA-target genes were identified. Functional annotation analysis showed that Apoptosis and NOD-like receptor signaling pathway and adaptive immune response were significantly enriched (P < 0.05). Interestingly, apoptosis pathway was significantly enriched in S vs. C, while NOD-like receptor pathway was enriched in R vs. C (P < 0.05). Two miRNAs, gga-miR-101-3p and gga-miR-155, in the hub positions of the miRNA-mRNA regulatory network, were identified as candidates potentially associated with SE infection. These 2 miRNAs directly repressed luciferase reporter gene activity via binding to 3′-untranslated regions of immune-related genes IRF4 and LRRC59; over-expressed gga-miR-155 and interference gga-miR-101-3p in chicken HD11 macrophage cells significantly altered expression of their target genes and decreased the production of pro-inflammatory cytokines. These findings facilitate better understanding of the mechanisms of host resistance and susceptibility to SE infection in chickens.

show abstract

The BIG Data Center: from deposition to integration to translation

Cited by 464 publications

References 49 publications

5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader

5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader

TMCO1 is essential for ovarian follicle development by regulating ER Ca2+ store of granulosa cells

Splenic microRNA Expression Profiles and Integration Analyses Involved in Host Responses to Salmonella enteritidis Infection in Chickens

Contact Info

Product

Resources

About