Regulatory analysis of the C. elegans genome with spatiotemporal resolution

Abstract

Summary Discovering the structure and dynamics of transcriptional regulatory events in the genome with cellular and temporal resolution is crucial to understanding the regulatory underpinnings of development and disease. We determined the genomic distribution of binding sites for 92 transcription factors (TFs) and regulatory proteins across multiple stages of C. elegans development by performing 241 ChIP-seq experiments. Integrating regulatory binding and cellular-resolution expression data yielded a spatiotemporally-resolved metazoan TF binding map. Using this map, we explore developmental regulatory circuits that encode combinatorial logic at the levels of co-binding and co-expression of TFs, characterizing (1) the genomic coverage and clustering of regulatory binding, (2) the binding preferences of and biological processes regulated by TFs, (3) the global TF co-associations and genomic subdomains that suggest shared patterns of regulation, and (4) key TFs and TF co-associations for fate specification of individual lineages and cell-types.

Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles

“…Systematic studies of chromatin composition across the genome have identified specific histone variants [20] or histone post-translational modifications [21][22][23] enriched at or around active enhancers. These stereotypic marks (such as H3K27ac/H3K4me1) have been extensively used to predict location of enhancer elements in a variety of tissues and organisms [24][25][26][27][28] and experimental validations confirmed to a large extent the validity of such approaches. The surprising observation that enhancers produce non-coding RNAs when they are active [29] even if the mechanisms and functional purpose of these eRNAs is yet unclear, provides nonetheless an interesting way to identify active enhancers [30,31].…”

Functional and Phylogenetic Characterization of Proteins Detected in Various Nematode Intestinal Compartments*

“…Transcription Factor Binding Site Motif Enrichment-Transcription factor (TF) consensus binding site (motif) enrichment and annotation was performed similarly to our previous study on tissue-specific overexpression in A. suum (15), but with a much more expansive reference database containing rich annotation for C. elegans (33). A maximum length of 2000bp 5Ј upstream regions (URs) were extracted for each gene based on the A. suum genome annotation, with shorter lengths where URs reached the end of a scaffold or overlapped with other coding sequences on either strand (12).…”

“…A maximum length of 2000bp 5Ј upstream regions (URs) were extracted for each gene based on the A. suum genome annotation, with shorter lengths where URs reached the end of a scaffold or overlapped with other coding sequences on either strand (12). In C. elegans, this UR length covers more than 91% of promoters (33), so this length was chosen to reduce background noise while maintaining a large proportion of promoters. Motif enrichment was performed using a discriminative motif analysis algorithm (DREME (34), using an 8-nucleotide maximum sequence search and 1000 generalized REs to increase accuracy), where the 5Ј URs of the genes corresponding to the proteins within a compartment were compared with the 5Ј URs of all other genes.…”

“…4; See Experimental Procedures). Motifs were associated with putative transcription factors by comparing to predicted motifs from the C. elegans regulatory analysis portion of the modENCODE project, which included predicted consensus binding sequences for 71.4% of known C. elegans TFs (33). In addition, known C. elegans motifs from JASPAR (36) and UniProbe (37) were included in the search, as well as vertebrate and mouse (respectively) sequences from the same databases.…”

E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response

“…Another possibility is that loss of HSF-1 is compensated for by other transcription factors, as HSF-1-binding sites in development overlap extensively with the extreme highly occupied target (xHOT) regions that are bound by many transcription factors (P = 3.2 × 10 −156 ) (Supplemental Fig. S4B) identified by modEN-CODE ChIP-seq analyses (Araya et al 2014). It has been proposed that genes with essential cellular functions are located in xHOT regions and redundantly regulated by multiple transcription factors to ensure proper levels of expression (Gerstein et al 2010;Van Nostrand and Kim 2013).…”