Imperial College London


Faculty of MedicineInstitute of Clinical Sciences

Professor of Computational Biology



+44 (0)20 3313 8353b.lenhard Website




Mr Alastair Douglas Ivor Williams +44 (0)20 3313 4318




230ICTEM buildingHammersmith Campus






BibTex format

author = {Cvetesic, N and Leitch, HG and Borkowska, M and Mueller, F and Carninci, P and Hajkova, P and Lenhard, B},
doi = {10.1101/gr.235937.118},
journal = {Genome Research},
pages = {1943--1956},
title = {SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA},
url = {},
volume = {28},
year = {2018}

RIS format (EndNote, RefMan)

AB - Cap analysis of gene expression (CAGE) is a methodology for genome-wide quantitative mapping of mRNA 5′ ends to precisely capture transcription start sites at a single nucleotide resolution. In combination with high-throughput sequencing, CAGE has revolutionized our understanding of rules of transcription initiation, led to discovery of new core promoter sequence features and discovered transcription initiation at enhancers genome-wide. The biggest limitation of CAGE is that even the most recently improved version (nAnT-iCAGE) still requires large amounts of total cellular RNA (5 micrograms), preventing its application to scarce biological samples such as those from early embryonic development or rare cell types. Here, we present SLIC-CAGE, a Super-Low Input Carrier-CAGE approach to capture 5′ ends of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity is achieved by specially designed, selectively degradable carrier RNA. We demonstrate the ability of SLIC-CAGE to generate data for genome-wide promoterome with 1000-fold less material than required by existing CAGE methods by generating a complex, high quality library from mouse embryonic day (E) 11.5 primordial germ cells.
AU - Cvetesic,N
AU - Leitch,HG
AU - Borkowska,M
AU - Mueller,F
AU - Carninci,P
AU - Hajkova,P
AU - Lenhard,B
DO - 10.1101/gr.235937.118
EP - 1956
PY - 2018///
SN - 1088-9051
SP - 1943
TI - SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
T2 - Genome Research
UR -
UR -
UR -
VL - 28
ER -