Thursday, December 11, 2014 3:41:03 PM
A new review article offers a nice overview of attempts to characterize the transcriptome of human stem cells using RNA-seq, the Iso-Seq™ method, and more. Kin Fai Au and Vittorio Sebastiano, scientists at the University of Iowa and Stanford University, respectively, contributed the review to Current Opinion in Genetics & Development.
“The introduction of the RNA-Seq technology based on [second-generation sequencing technology] has provided a remarkable step forward providing a fast and inexpensive way to determine the transcriptome of a given cell type and several remarkable works have been done using this type of approach,” Au and Sebastiano write. “Nonetheless tasks like de novo discovery of genes, gene isoforms assembly or transcript and isoform abundance determination are still challenging and far from being achieved.”
They report on a previous paper from Au in which Single Molecule, Real-Time (SMRT®) Sequencing was combined with short-read sequencing to detect isoforms in a well-characterized human embryonic stem cell line. Long reads led to the detection of hundreds of novel isoforms and long noncoding RNAs. Long intergenic noncoding RNAs (lincRNAs) are a topic of interest in the review article, where Au and Sebastiano note that they “have a very high degree of repetitive elements and it is therefore extremely challenging to determine the correct gene annotation and the abundance due to the difficulties in aligning short read data to the genome.” With long-read sequencing, they add, sequence data spans unique sections of the lincRNAs and makes it possible to accurately map reads to the correct region.
The authors cite recent studies demonstrating more transcriptional activity in the human genome than has been expected. “Transcription occurs across 80–90% of the human genome, in contrast with the assumption that only 3% (or less) of the genome is actually coding for proteins,” they write. LincRNAs and other noncoding RNAs may explain the difference between those numbers.
Au and Sebastiano call for more studies of stem cells using long-read sequencing technology to establish a better view of the transcriptional activity in these important cells with accurate detection of noncoding RNAs characterized by highly repetitive sequence. “Given such complexity of the epigenetic status for most of the genes, it is essential to identify the transcripts and the isoforms that are indeed functionally relevant (even if expressed at low levels) in [pluripotent stem cells],” they write. http://blog.pacificbiosciences.com/2014/12/review-article-long-read-sequencing.html
Recent PACB News
- Ambry Genetics and PacBio Announce Collaboration to Sequence Up to 7,000 Human Genomes Aimed at Providing Answers for Families Battling Rare Diseases • PR Newswire (US) • 05/15/2024 01:45:00 PM
- Form S-3ASR - Automatic shelf registration statement of securities of well-known seasoned issuers • Edgar (US Regulatory) • 05/09/2024 08:33:12 PM
- Form 10-Q - Quarterly report [Sections 13 or 15(d)] • Edgar (US Regulatory) • 05/09/2024 08:21:46 PM
- Form 8-K - Current report • Edgar (US Regulatory) • 05/09/2024 08:12:15 PM
- PacBio Announces First Quarter 2024 Financial Results • PR Newswire (US) • 05/09/2024 08:05:00 PM
- PacBio Announces Preliminary First Quarter 2024 Revenue and Updates 2024 Revenue Guidance • PR Newswire (US) • 04/16/2024 12:05:00 PM
- Estonia National Biobank Selects PacBio to Sequence 10,000 Whole Genomes • PR Newswire (US) • 03/27/2024 12:00:00 PM
- PacBio Grants Equity Incentive Award to New Employee • PR Newswire (US) • 03/22/2024 08:30:00 PM
- PacBio Announces PureTarget™ Repeat Expansion Panel, Expanding its Portfolio of End-to-End Clinical Research Solutions • PR Newswire (US) • 03/12/2024 01:05:00 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 03/06/2024 10:36:07 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 03/06/2024 10:30:18 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 03/06/2024 10:26:40 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 03/06/2024 10:22:45 PM
- Form 144 - Report of proposed sale of securities • Edgar (US Regulatory) • 03/04/2024 11:32:39 PM
- Form 144 - Report of proposed sale of securities • Edgar (US Regulatory) • 03/04/2024 11:22:32 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 02/26/2024 09:55:28 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 02/26/2024 09:36:09 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 02/26/2024 09:25:48 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 02/26/2024 09:19:42 PM
- PacBio to Present at Upcoming Investor Conferences • PR Newswire (US) • 02/26/2024 09:05:00 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 02/21/2024 11:25:13 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 02/21/2024 11:20:57 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 02/21/2024 11:17:14 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 02/21/2024 11:07:18 PM
- Form 144 - Report of proposed sale of securities • Edgar (US Regulatory) • 02/20/2024 09:17:12 PM
Greenlite Ventures Inks Deal to Acquire No Limit Technology • GRNL • May 17, 2024 3:00 PM
Music Licensing, Inc. (OTC: SONG) Subsidiary Pro Music Rights Secures Final Judgment of $114,081.30 USD, Demonstrating Strength of Licensing Agreements • SONGD • May 17, 2024 11:00 AM
VPR Brands (VPRB) Reports First Quarter 2024 Financial Results • VPRB • May 17, 2024 8:04 AM
ILUS Provides a First Quarter Filing Update • ILUS • May 16, 2024 11:26 AM
Cannabix Technologies and Omega Laboratories Inc. enter Strategic Partnership to Commercialize Marijuana Breathalyzer Technology • BLO • May 16, 2024 8:13 AM
Avant Technologies to Revolutionize Data Center Management with Proprietary AI Software Platform • AVAI • May 16, 2024 8:00 AM