Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

Genome Research - Tập 18 Số 4 - Trang 610-621 - 2008
Ryan D. Morin1, Michael D. O’Connor, Malachi Griffith, Florian Kuchenbauer, Allen Delaney, Anna‐Liisa Prabhu, Yongjun Zhao, Helen McDonald, Thomas Zeng, Martin Hirst, Connie J. Eaves, Marco A. Marra
1Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.

Tóm tắt

MicroRNAs (miRNAs) are emerging as important, albeit poorly characterized, regulators of biological processes. Key to further elucidation of their roles is the generation of more complete lists of their numbers and expression changes in different cell states. Here, we report a new method for surveying the expression of small RNAs, including microRNAs, using Illumina sequencing technology. We also present a set of methods for annotating sequences deriving from known miRNAs, identifying variability in mature miRNA sequences, and identifying sequences belonging to previously unidentified miRNA genes. Application of this approach to RNA from human embryonic stem cells obtained before and after their differentiation into embryoid bodies revealed the sequences and expression levels of 334 known plus 104 novel miRNA genes. One hundred seventy-one known and 23 novel microRNA sequences exhibited significant expression differences between these two developmental states. Owing to the increased number of sequence reads, these libraries represent the deepest miRNA sampling to date, spanning nearly six orders of magnitude of expression. The predicted targets of those miRNAs enriched in either sample shared common features. Included among the high-ranked predicted gene targets are those implicated in differentiation, cell cycle control, programmed cell death, and transcriptional regulation.

Từ khóa


Tài liệu tham khảo

10.1093/hmg/ddh068

10.1016/j.febslet.2005.08.009

10.1126/science.1142612

10.1038/75556

10.1101/gr.7.10.986

10.1093/bioinformatics/bth088

10.1038/ng1794

10.1038/ng1914

10.1038/ng1253

10.1182/blood-2003-09-3314

10.1186/1471-213X-5-22

10.1016/j.cell.2005.08.020

10.1261/rna.7135204

10.1007/s00335-007-9032-6

10.1073/pnas.0511155103

Davison,, 2006, Analyzing micro-RNA expression using microarrays, Methods Enzymol., 411, 14, 10.1016/S0076-6879(06)11002-2

10.1093/humrep/deh529

10.1371/journal.pone.0000219

10.1126/science.1122689

Griffiths-Jones,, 2006, miRBase: The microRNA sequence database, Methods Mol. Biol., 342, 129

10.1016/j.molcel.2007.06.017

10.1186/gb-2007-8-6-r113

10.1093/nar/gkg599

10.1016/S1534-5807(03)00227-2

Itskovitz-Eldor,, 2000, Differentiation of human embryonic stem cells into embryoid bodies compromising the three embryonic germ layers, Mol. Med., 6, 88, 10.1007/BF03401776

10.1093/nar/gkm368

10.1371/journal.pbio.0020363

10.1371/journal.pbio.0050057

10.1126/science.1138050

10.1093/nar/gkm696

10.1016/j.cell.2007.04.040

10.1016/j.cell.2004.12.035

10.1126/science.1090599

Margulies,, 2005, Genome sequencing in microfabricated high-density picolitre reactors, Nature, 437, 376, 10.1038/nature03959

10.1093/nar/gkj077

10.1261/rna.223807

10.1093/nar/gkl428

10.1371/journal.pcbi.0020033

10.1038/nmeth746

10.1158/0008-5472.CAN-07-0533

10.1101/gad.1476406

10.1016/j.cell.2006.10.040

10.1016/S0012-1606(03)00256-2

10.1182/blood-2006-01-030015

10.1634/stemcells.2004-0341

10.1002/bdrc.20070

10.1007/s00335-006-0025-7

10.1016/j.ydbio.2004.02.019

10.1038/ng1969

10.1101/gad.1425706

10.1186/1471-2105-6-310

10.1186/gb-2007-8-6-r96

10.1007/s00018-005-5467-7

10.1007/s00381-006-0173-9

Thông tin
Thông tin xuất bản

Genome Research

Tập 18 Số 4

610-621

Thông tin tác giả