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Nat Biotechnol DOI:10.1038/nbt.2450

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Publication TypeJournal Article
Year of Publication2013
AuthorsTrapnell, C, Hendrickson, DG, Sauvageau, M, Goff, L, Rinn, JL, Pachter, L
JournalNat Biotechnol
Date Published2013 Jan
KeywordsFibroblasts, Gene Expression Regulation, HeLa Cells, Homeodomain Proteins, Humans, Lung, RNA, Messenger, Sequence Analysis, RNA, Transcription Factors

Differential analysis of gene and transcript expression using high-throughput RNA sequencing (RNA-seq) is complicated by several sources of measurement variability and poses numerous statistical challenges. We present Cuffdiff 2, an algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. Cuffdiff 2 robustly identifies differentially expressed transcripts and genes and reveals differential splicing and promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1, which we show is required for lung fibroblast and HeLa cell cycle progression. Loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle. Cuffdiff 2 performs robust differential analysis in RNA-seq experiments at transcript resolution, revealing a layer of regulation not readily observable with other high-throughput technologies.


Alternate JournalNat. Biotechnol.
PubMed ID23222703
PubMed Central IDPMC3869392
Grant ListDP2 OD006670 / OD / NIH HHS / United States
P01 GM099117 / GM / NIGMS NIH HHS / United States
R01 HG006129 / HG / NHGRI NIH HHS / United States
P01GM099117 / GM / NIGMS NIH HHS / United States
P50 HG006193 / HG / NHGRI NIH HHS / United States
R01 ES020260 / ES / NIEHS NIH HHS / United States
DP2OD006670 / OD / NIH HHS / United States
P50HG006193 / HG / NHGRI NIH HHS / United States
R01 DK094699 / DK / NIDDK NIH HHS / United States
R01ES020260 / ES / NIEHS NIH HHS / United States