Evolution of promoter-proximal pausing enabled a new layer of transcription control.

Promoter-proximal pausing of RNA polymerase II (Pol II) is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here we analyzed transcription in species across the tree of life.

Widespread priming of transcriptional regulatory elements by incipient accessibility or RNA polymerase II pause in early embryos of the sea urchin Strongylocentrotus purpuratus.

Transcriptional regulatory elements (TREs) are the primary nodes that control developmental gene regulatory networks. In embryo stages, larvae, and adult differentiated red spherule cells of the sea urchin Strongylocentrotus purpuratus, transcriptionally engaged TREs are detected by Precision Run-On Sequencing (PRO-seq), which maps genome-wide at base pair resolution the location of paused or elongating RNA polymerase II (Pol II). In parallel, TRE accessibility is estimated by the Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq).

Evolution of promoter-proximal pausing enabled a new layer of transcription control.

Promoter-proximal pausing of RNA polymerase II (Pol II) is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here we analyzed transcription in species across the tree of life.

Identification and prediction of developmental enhancers in sea urchin embryos.

Background: The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging, even in tractable model organisms like sea urchins.

Results: We evaluate the use of chromatin accessibility, transcription and RNA Polymerase II for their ability to predict enhancer activity of genomic regions in sea urchin embryos.

Electron microscopic characterization of nuclear egress in the sea urchin gastrula.

Nuclear egress, also referred to as nuclear envelope (NE) budding, is a process of transport in which vesicles containing molecular complexes or viral particles leave the nucleus through budding from the inner nuclear membrane (INM) to enter the perinuclear space. Following this event, the perinuclear vesicles (PNVs) fuse with the outer nuclear membrane (ONM), where they release their contents into the cytoplasm. Nuclear egress is thought to participate in many functions such as viral replication, cellular differentiation, and synaptic development.

The origins of developmental gene regulation.

The leap from simple unicellularity to complex multicellularity remains one of life's major enigmas. The origins of metazoan developmental gene regulatory mechanisms are sought by analyzing gene regulation in extant eumetazoans, sponges, and unicellular organisms. The main hypothesis of this manuscript is that, developmental enhancers evolved from unicellular inducible promoters that diversified the expression of regulatory genes during metazoan evolution.

Transcriptional and post-transcriptional regulation of histone variant H2A.Z during sea urchin development.

Histone variant H2A.Z promotes chromatin accessibility at transcriptional regulatory elements and is developmentally regulated in metazoans. We characterize the transcriptional and post-transcriptional regulation of H2A.

Expression of GATA and POU transcription factors during the development of the planktotrophic trochophore of the polychaete serpulid Hydroides elegans.

The expression of transcription factors with endodermal and mesodermal roles in bilaterians is characterized during the development of Hydroides elegans, a serpulid polychaete with planktotrophic trochophore. GATA 4/5/6 is expressed in endodermal and mesodermal precursors during embryogenesis and in the midgut of trochophore larvae. HeGATA1/2/3a is expressed in animal hemisphere blastomeres 1d121 and 1d122, in dorsal ectoderm and in 4d endomesodermal derivatives that maintain their expression in trochophore larvae.

Developmental control of transcriptional and proliferative potency during the evolutionary emergence of animals.

It is proposed that the evolution of complex animals required repressive genetic mechanisms for controlling the transcriptional and proliferative potency of cells. Unicellular organisms are transcriptionally potent, able to express their full genetic complement as the need arises through their life cycle, whereas differentiated cells of multicellular organisms can only express a fraction of their genomic potential. Likewise, whereas cell proliferation in unicellular organisms is primarily limited by nutrient availability, cell proliferation in multicellular organisms is developmentally regulated.

Development of a feeding trochophore in the polychaete Hydroides elegans.

Hydroides elegans is an indirectly developing polychaete with equal spiral cleavage, gastrulation by invagination, and a feeding trochophore. Expression of several transcription factors and differentiation genes has been characterized. Comparative analysis reveals evolutionarily conserved roles.

Brachyury, Tbx2/3 and sall expression during embryogenesis of the indirectly developing polychaete Hydroides elegans.

Expression of the transcription factor genes brachyury, Tbx2/3 and sall is characterized in detail for the first time in an indirectly developing spiralian with a feeding trochophore. In Hydroides elegans, gut formation proceeds by invagination during embryogenesis and is followed by feeding-dependent posterior growth during larval stages. Posterior growth gives rise to the reproductive and segmented portion of the adult and derives primarily from multipotent dorsal blastomeres.

Indirect development, transdifferentiation and the macroregulatory evolution of metazoans.

It is proposed here that a biphasic life cycle with partial dedifferentiation of intermediate juvenile or larval stages represents the mainstream developmental mode of metazoans. Developmental plasticity of differentiated cells is considered the essential characteristic of indirect development, rather than the exclusive development of the adult from 'set-aside' cells. Many differentiated larval cells of indirect developers resume proliferation, partially dedifferentiate and contribute to adult tissues.

The transcription factors HeBlimp and HeT-brain of an indirectly developing polychaete suggest ancestral endodermal, gastrulation, and sensory cell-type specification roles.

The expression of Blimp and T-brain was characterized during embryogenesis of the indirectly developing polychaete Hydroides elegans. The expression of both genes in the vegetal blastomeres of this lophotrochozoan is restricted to the lateral and oral regions of the blastopore. Both transcription factors also have expression patterns consistent with ancestral neural functions.

Histone H2A.Z expression in two indirectly developing marine invertebrates correlates with undifferentiated and multipotent cells.

The embryos of indirect developers generate an intermediate larval stage that nourishes the proliferation of undifferentiated multipotent cell precursors in charge of postembryonic adult formation. Multipotency affects the regulation of many genes and seems to be mediated in part by chromatin modification. Chromatin transcriptional properties are regulated by histone modification and by incorporation of peculiar histone variants.

Sinistral equal-size spiral cleavage of the indirectly developing polychaete Hydroides elegans.

Two major variants of the stereotypic spiral cleavage correlate with distinct developmental modes in polychaetes. Indirect development through a feeding trochophore larva correlates with development from four equal-sized blastomeres, whereas direct development correlates with unequal cleavage characterized by a large dorsal blastomere precursor maternally predetermined. The equal-size spiral cleavage of the indirectly developing serpulid Hydroides elegans has been reconstructed from serial sections of nuclei-stained embryos.

HeOtx expression in an indirectly developing polychaete correlates with gastrulation by invagination.

The expression of an Otx homolog in the indirectly developing polychaete Hydroides elegans was characterized during embryo, trochophore, and feeding-larva stages. In the animal hemisphere, HeOtx is first expressed in 1q(12) blastomeres and their immediate descendants. Such discrete embryonic animal hemisphere Otx expression perhaps relates to cell-type specification functions of the larva.

Ciliary band gene expression patterns in the embryo and trochophore larva of an indirectly developing polychaete.

The trochophore larvae of indirectly developing spiralians have ciliary bands with motor and feeding functions. The preoral prototroch ciliary band is the first differentiating organ in annelid and mollusk embryos. Here we report the expression of several ciliary band markers during embryogenesis and early larval stages of the indirectly developing polychaete Hydroides elegans.

Embryonic expression of HeFoxA1 and HeFoxA2 in an indirectly developing polychaete.

Two forkhead family transcription factors, HeFoxA1 and HeFoxA2, were isolated from the serpulid annelid Hydroides elegans and their transcript distribution were characterized during embryogenesis. HeFoxA1 is first detected in second quartet blastomeres soon after their formation, and later in all vegetal half blastomeres, which comprise ectoderm, endoderm, and mesoderm precursors. HeFoxA1 expression declines first in subtrochal ectoderm and presumptive midgut precursors, as well as apparently in D quadrant blastomeres in advance of any known signaling events.

Hindgut specification and cell-adhesion functions of Sphox11/13b in the endoderm of the sea urchin embryo.

Sphox11/13b is one of the two hox genes of Strongylocentrotus purpuratus expressed in the embryo. Its dynamic pattern of expression begins during gastrulation, when the transcripts are transiently located in a ring of cells at the edge of the blastopore. After gastrulation, expression is restricted to the anus-hindgut region at the boundary between the ectoderm and the endoderm.

Unusual gene order and organization of the sea urchin hox cluster.

While the highly consistent gene order and axial colinear patterns of expression seem to be a feature of vertebrate hox gene clusters, this pattern may be less well conserved across the rest of the bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3' gene is Hox5.

Expression patterns of four different regulatory genes that function during sea urchin development.

The spatial and temporal expression patterns of Strongylocentrotus purpuratus genes encoding four different transcription factors, viz. SpFoxb, SpHes, SpKrl, and SpNk1, have been examined, using a recently developed, highly sensitive whole mount in situ hybridization procedure, and quantitative real time PCR. Two of the genes studied, SpHes and SpNk1, are newly isolated.

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.

We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.

A genomic regulatory network for development.

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology.