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Method: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
- Kyung Yeon Han,
- Kyu-Tae Kim,
- Je-Gun Joung,
- Dae-Soon Son,
- Yeon Jeong Kim,
- Areum Jo,
- Hyo-Jeong Jeon,
- Hui-Sung Moon,
- Chang Eun Yoo,
- Woosung Chung,
- Hye Hyeon Eum,
- Sangmin Kim,
- Hong Kwan Kim,
- Jeong Eon Lee,
- Myung-Ju Ahn,
- Hae-Ock Lee,
- Donghyun Park,
- and Woong-Yang Park
Genome Res. January 2018 28: 75-87; Published in Advance December 5, 2017, doi:10.1101/gr.223263.117
...expression regulation and significant cell-to-cell heterogeneity, unveiling the causal relationships between genomic variations and mRNA transcription profiles turned out to be very challenging (Altschuler and Wu 2010; Han et al. 2014). Thus, there is a growing demand to integrate DNA and RNA analyses...
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Research: APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication
- Vladimir B. Seplyarskiy,
- Ruslan A. Soldatov,
- Konstantin Y. Popadin,
- Stylianos E. Antonarakis,
- Georgii A. Bazykin,
- and Sergey I. Nikolaev
Genome Res. February 2016 26: 174-182; Published in Advance January 11, 2016, doi:10.1101/gr.197046.115
...can also be a source of DNA damage and mutations. Recently, it was shown that some homologs of APOBEC (apolipoprotein B mRNA-editing e nzyme, c atalytic polypeptide-like), cytidine deaminases that function as viral protecting agents as well as in RNA editing, may be a major factor causing mutations...
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Method: A novel approach for data integration and disease subtyping
- Tin Nguyen,
- Rebecca Tagett,
- Diana Diaz,
- and Sorin Draghici
Genome Res. December 2017 27: 2025-2039; Published in Advance October 24, 2017, doi:10.1101/gr.215129.116
...invasive carcinoma (BRCA), and colon adenocarcinoma (COAD). We used mRNA expression, DNA methylation, and miRNA expression data for each of the six cancers. TCGA contains multiple platform for each data type. We chose the platforms giving the largest set of common tumor samples across the three data types...
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Research: A functional methylome map of ulcerative colitis
- Robert Häsler,
- Zhe Feng,
- Liselotte Bäckdahl,
- Martina E. Spehlmann,
- Andre Franke,
- Andrew Teschendorff,
- Vardhman K. Rakyan,
- Thomas A. Down,
- Gareth A. Wilson,
- Andrew Feber,
- Stephan Beck,
- Stefan Schreiber,
- and Philip Rosenstiel
Genome Res. November 2012 22: 2130-2137; Published in Advance July 23, 2012, doi:10.1101/gr.138347.112
...tissue from the intestinal mucosa (Table 1, validation panel I and II). This was performed by pyrosequencing (bisulfite-modified DNA, n = 50 individuals) for methylation analysis and TaqMan-based realtime PCR (n = 135 individuals) for differential mRNA expression. Significance criteria were defined...
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Research: Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
- Andrew Feber,
- Gareth A. Wilson,
- Lu Zhang,
- Nadege Presneau,
- Bernadine Idowu,
- Thomas A. Down,
- Vardhman K. Rakyan,
- Luke A. Noon,
- Alison C. Lloyd,
- Elia Stupka,
- Vassia Schiza,
- Andrew E. Teschendorff,
- Gary P. Schroth,
- Adrienne Flanagan,
- and Stephan Beck
Genome Res. April 2011 21: 515-524; Published in Advance February 1, 2011, doi:10.1101/gr.109678.110
..., University College London, London WC1E 6BT, United Kingdom Abstract Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However...
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LETTER: Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
- Vitalina M. Komashko,
- Luis G. Acevedo,
- Sharon L. Squazzo,
- Sushma S. Iyengar,
- Alina Rabinovich,
- Henriette O’Geen,
- Roland Green,
- and Peggy J. Farnham
Genome Res. April 2008 18: 521-532; Published in Advance March 17, 2008, doi:10.1101/gr.074609.107
...in housekeeping functions such as DNA replication, mRNA processing, or protein translation show little cell type-specific expression ( Schadt et al. 2004 ). On the other hand, genes that encode proteins that confer highly specific phenotypes (such as detoxification enzymes in hepatocytes or self...
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Method: Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
- Hidenori Tani,
- Rena Mizutani,
- Kazi Abdus Salam,
- Keiko Tano,
- Kenichi Ijiri,
- Ai Wakamatsu,
- Takao Isogai,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. May 2012 22: 947-956; Published in Advance February 27, 2012, doi:10.1101/gr.130559.111
...of most ncRNAs are unclear, and novel techniques that can distinguish functional ncRNAs are needed. Studies of mRNAs have revealed that the half-life of each mRNA is closely related to its physiological function, raising the possibility that the RNA stability of an ncRNA reflects its function...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...clinical practice.A hallmark of cancer is widespread genetic and epigenetic instability (Hanahan and Weinberg 2011). Cancer often originates through somatic mutations that accumulate throughout an individual's lifetime due to exposure to carcinogens, DNA replication errors, and other factors, thereby...
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