TELP, a sensitive and versatile library construction method for next-generation sequencing

Xu, Peng; Wu, Jingyi; Brunmeir, Reinhard; Kim, Sun-Yee; Zhang, Qiongyi; Ding, Chunming; Han, Weiping; Xie, Wei; Xu, Feng

doi:10.1093/nar/gku818

Cited by 46 publications

(42 citation statements)

References 33 publications

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“…To construct ChIP-seq libraries, we employed a method described previously [55]. In short, 5ng of ChIP DNA were used as starting material.…”

Section: Methodsmentioning

confidence: 99%

Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis

Brunmeir

et al. 2016

PLoS Genet

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Increasing energy expenditure through brown adipocyte recruitment is a promising approach to combat obesity. We report here the comprehensive profiling of the epigenome and transcriptome throughout the lineage commitment and differentiation of C3H10T1/2 mesenchymal stem cell line into brown adipocytes. Through direct comparison to datasets from differentiating white adipocytes, we systematically identify stage- and lineage-specific coding genes, lncRNAs and microRNAs. Utilizing chromatin state maps, we also define stage- and lineage-specific enhancers, including super-enhancers, and their associated transcription factor binding motifs and genes. Through these analyses, we found that in brown adipocytes, brown lineage-specific genes are pre-marked by both H3K4me1 and H3K27me3, and the removal of H3K27me3 at the late stage is necessary but not sufficient to promote brown gene expression, while the pre-deposition of H3K4me1 plays an essential role in poising the brown genes for expression in mature brown cells. Moreover, we identify SOX13 as part of a p38 MAPK dependent transcriptional response mediating early brown cell lineage commitment. We also identify and subsequently validate PIM1, SIX1 and RREB1 as novel regulators promoting brown adipogenesis. Finally, we show that SIX1 binds to adipogenic and brown marker genes and interacts with C/EBPα, C/EBPβ and EBF2, suggesting their functional cooperation during adipogenesis.

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“…To construct ChIP-seq libraries, we employed a method described previously [55]. In short, 5ng of ChIP DNA were used as starting material.…”

Section: Methodsmentioning

confidence: 99%

Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis

Brunmeir

et al. 2016

PLoS Genet

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“…Endogenous 5fC was blocked by hydroxylamine, and endogenous 5hmC was oxidized to 5fC using K2RuO4. The newly generated 5fC was labelled with 5-(2-azidoethyl)-1,3-indandione (AI) (J&K, 2793948), and the AI-labeled ssDNA was used directly for library preparation with the TELP protocol 39 . It is worth mentioning that we designed a homemade adapter with a unique molecular identifier (UMI) for deduplication 40 .…”

Section: Genomic Dna Library Construction and Sequencingmentioning

confidence: 99%

Tissue-specific 5-hydroxymethylcytosine landscape of the human genome

Zhang

et al. 2020

Preprint

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5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark that regulates gene expression. Charting the landscape of 5hmC in human tissues is fundamental to understand its regulatory functions. Here, we systematically profiled the whole-genome 5hmC landscape at single-base resolution for 19 types of human tissues. We found that 5hmC preferentially decorates gene bodies and outperforms gene body 5mC in reflecting gene expression. Approximately one-third of 5hmC peaks are tissue-specific differentially hydroxymethylated regions (tsDhMRs), which are deposited in regulatory elements that regulate the expression of nearby tissue-specific functional genes. In addition, tsDhMRs are enriched with tissue-specific transcription-factor-binding sites and may rewire tissue-specific gene expression networks. Moreover, tsDhMRs are associated with SNPs identified by genome-wide association study (GWAS), linked to tissue-specific phenotypes and diseases. Collectively, our results show the tissue-specific 5hmC landscape of the human genome and demonstrate that 5hmC serves as a fundamental regulatory element affecting tissue-specific development and diseases.

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“…The histone and DNA solution was incubated with 1μg H3K27ac (Active motif, 39133) or H3K4me3 (homemade 77 ) overnight. After eluting DNA from histone and repairing dephosphorylate 3' end, the resulting DNA was subjected to TELP library preparation as described 78 .…”

Section: Chipseq Experimentsmentioning

confidence: 99%

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

Argelaguet¹,

Mohammed²,

Clark³

et al. 2019

Preprint

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Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNAsequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell tripleomics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineagespecific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers. Highlights• First map of mouse gastrulation using comprehensive single cell tripleomic analysis.• Exit from pluripotency is associated with a global repressive epigenetic landscape, driven by a sharp gain of DNA methylation and a gradual decrease of chromatin accessibility. • DNA methylation and chromatin accessibility changes in enhancers, but not in promoters, are associated with germ layer formation. • Mesoderm and endoderm enhancers become open and demethylated upon lineage commitment. • Ectoderm enhancers are primed in the early epiblast and protected from the global repressive dynamics, supporting a default model of ectoderm commitment in vivo . 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86In mammals, specification of the basic body plan occurs during gastrulation, when a singlelayered blastula is reorganised to give rise to the three primary germ layers: the ectoderm, mesoderm and endoderm 1,2 . Recent advances in singlecell RNA sequencing have facilitated unbiased and comprehensive characterisation of such developmental trajectories in a variety of different systems 3-5 . However, while gene expression dynamics of mouse development have been characterized in detail 6-12 , the role of the epigenome in cell fate decisions in early development remains poorly understood 13 .The period of mouse development prior to gastrulation is characterised by extensive remodelling of the epigenome [14][15][16][17][18][19][20][21][22][23...

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TELP, a sensitive and versatile library construction method for next-generation sequencing

Cited by 46 publications

References 33 publications

Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis

Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis

Tissue-specific 5-hydroxymethylcytosine landscape of the human genome

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

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