UHRF1 regulation of Dnmt1 is required for pre-gastrula zebrafish development

Kent, Brandon; Magnani, Elena; Walsh, Martin J.; Sadler, Kirsten C.

doi:10.1016/j.ydbio.2016.01.036

Cited by 27 publications

(35 citation statements)

References 56 publications

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“…RNA was isolated from zebrafish embryos via standard TRIzol protocol as described (Kent et al 2016). Reverse transcription was accomplished using the SuperScript III kit from Invitrogen with 2 µg total RNA.…”

Section: Rna Isolation Reverse Transcription and Rt-pcrmentioning

confidence: 99%

High resolution annotation of zebrafish transcriptome using long-read sequencing

et al. 2018

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With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited, however, by gaps in zebrafish annotation, which are especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short-read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the transcriptome of zebrafish embryos before and after ZGA. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2539 high-confidence novel transcripts that originated from previously unannotated loci and 1835 high-confidence new isoforms in previously annotated genes. We validated these findings using a suite of computational approaches including structural prediction, sequence homology, and functional conservation analyses, as well as by confirmatory transcript quantification with short-read sequencing data. Our analyses provided insight into new homologs and paralogs of functionally important proteins and noncoding RNAs, isoform switching occurrences, and different classes of novel splicing events. Several novel isoforms representing distinct splicing events were validated through PCR experiments, including the discovery and validation of a novel 8-kb transcript spanning multiple elements, an important driver of early development. Our study provides a significantly improved zebrafish transcriptome annotation resource.

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Section: Rna Isolation Reverse Transcription and Rt-pcrmentioning

confidence: 99%

High resolution annotation of zebrafish transcriptome using long-read sequencing

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…RNA was isolated from zebrafish embryos via standard Trizol protocol as described (Kent et al 2016). Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA.…”

Section: Rna Isolation Reverse Transcription and Rt-pcrmentioning

confidence: 99%

High Resolution Annotation of Zebrafish Transcriptome Using Long-Read Sequencing

Nudelman

Frasca

Kent

et al. 2017

Preprint

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With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited, however, by gaps in zebrafish annotation, which are especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study transcriptome of zebrafish embryos before and after ZGA. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 high confidence new isoforms in previously annotated genes. We validated these findings using a suite of computational approaches including structural prediction, sequence homology and functional conservation analyses, as well as by confirmatory transcript quantification with short-read sequencing data. Our analyses provided insight into new homologs and paralogs of functionally important proteins and non-coding RNAs, isoform switching occurrences and different classes of novel splicing events. Several novel isoforms representing distinct splicing events were validated through PCR experiments, including the discovery and validation of a novel 8 kb transcript spanning multiple miR-430 elements, an important driver of early development. Our study provides a significantly improved zebrafish transcriptome annotation resource.

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“…The sensing of hemi-methylated DNA by UHRF1, induces the recruitment of DNA methyltransferase 1 (DNMT1) which methylates the opposite unmethylated DNA strand, and consequently CpG dinucleotides are methylated on both strands. Through these properties, the tandem UHRF1/DNMT1 plays a role during cell proliferation and therefore in development and cancer [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

The epigenetic integrator UHRF1: on the road to become a universal biomarker for cancer

et al. 2017

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Cancer is one of the deadliest diseases in the world causing record number of mortalities in both developed and undeveloped countries. Despite a lot of advances and breakthroughs in the field of oncology still, it is very hard to diagnose and treat the cancers at early stages. Here in this review we analyze the potential of Ubiquitin-like containing PHD and Ring Finger domain 1 (UHRF1) as a universal biomarker for cancers. UHRF1 is an important epigenetic regulator maintaining DNA methylation and histone code in the cell. It is highly expressed in a variety of cancers and is a well-known oncogene that can disrupt the epigenetic code and override the senescence machinery. Many studies have validated UHRF1 as a powerful diagnostic and prognostic tool to differentially diagnose cancer, predict the therapeutic response and assess the risk of tumor progression and recurrence. Highly sensitive, non-invasive and cost effective approaches are therefore needed to assess the level of UHRF1 in patients, which can be deployed in diagnostic laboratories to detect cancer and monitor disease progression.

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UHRF1 regulation of Dnmt1 is required for pre-gastrula zebrafish development

Cited by 27 publications

References 56 publications

High resolution annotation of zebrafish transcriptome using long-read sequencing

High resolution annotation of zebrafish transcriptome using long-read sequencing

High Resolution Annotation of Zebrafish Transcriptome Using Long-Read Sequencing

The epigenetic integrator UHRF1: on the road to become a universal biomarker for cancer

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