Data from: Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments

Regulating transcription allows organisms to respond to their environment,
both within a single generation (plasticity) and across generations
(adaptation). We examined transcriptional differences in gill tissues of
fishes in the Poecilia mexicana species complex (family Poeciliidae),
which have colonized toxic springs rich in hydrogen sulfide (H2S) in
southern Mexico. There are gene expression differences between sulfidic
and non-sulfidic populations, yet regulatory mechanisms mediating this
gene expression variation remain poorly studied. We combined capped-small
RNA sequencing (csRNA-seq), which captures actively transcribed (i.e.,
nascent) transcripts, and traditional messenger RNA sequencing (mRNA-seq)
to examine how variation in transcription, enhancer activity, and
associated transcription factor binding sites may facilitate adaptation to
extreme environments. csRNA-seq revealed thousands of differentially
initiated transcripts between sulfidic and non-sulfidic populations, many
of which are involved in H2S detoxification and response. Analyses of
transcription factor binding sites in promoter and putative enhancer
csRNA-seq peaks identify a suite of transcription factors likely involved
in regulating H2S-specific shifts in gene expression, including several
key transcription factors known to respond to hypoxia. Our findings
uncover a complex interplay of regulatory processes that reflect the
divergence of extremophile populations of P. mexicana from their
non-sulfidic ancestors and suggest shared responses among evolutionarily
independent lineages.