December 30, 2013
To the Editors of Genome Research,
We are happy to submit our revised manuscript “Dynamic shifts in occupancy by TAL1
are guided by GATA factors and drive large-scale reprogramming of gene expression during
hematopoiesis” (MS ID#: GENOME/2013/164830) for consideration for publication in Genome
Research. This is a companion manuscript to a major integrative and comparative analysis of
epigenetic data in multiple cell types from the Mouse ENCODE Consortium. To my knowledge,
only it and the Pimkin et al. “Divergent functions of hematopoietic transcription factors in
lineage priming and differentiation during erythro-megakaryopoiesis” (MS ID#:
GENOME/2013/164178) are still under consideration at Genome Research.
We greatly appreciate the insightful reviews of our initial submission. While they were
highly supportive overall, both reviewers pointed to need for greater clarity in the presentation
and some further analyses. In response, we have revised the manuscript extensively, and the
major textual revisions are in blue text in the main manuscript. Several new panels to figures
were made and some new panels added in response to recommendations from the reviewers.
The Discussion is more focused on interpretation of the observations. We have also edited
throughout to streamline and clarify the presentation. The changes are described in more detail
in the document “Responses to Reviewers.”
The manuscript has been seen and approved by all the authors.
We hope that review of the revised manuscript will be by the previous reviewers.
All data have been deposited in GEO and data generated as part of mouse ENCODE are
on the UCSC Genome Browser.
Approved gene and protein names have been used throughout.
Thank you for considering our revised manuscript.
Sincerely,
Ross C. Hardison
304 Wartik Laboratory, Penn State University, University Park, PA 16802
e-mail: rch8@psu.edu
Phone: 814-863-0113