New 3-D model of a DNA-regulating complex in human cells provides cancer
clues

Date:
October 13, 2020
Source:
Dana-Farber Cancer Institute
Summary:
Scientists have created an unprecedented 3-dimensional structural
model of a key molecular 'machine' known as the BAF complex, which
modifies DNA architecture and is frequently mutated in cancer and
some other diseases.



FULL STORY ========================================================================== Scientists have created an unprecedented 3-dimensional structural model
of a key molecular "machine" known as the BAF complex, which modifies
DNA architecture and is frequently mutated in cancer and some other
diseases. The researchers, led by Cigall Kadoch, PhD, of Dana-Farber
Cancer Institute, have reported the first 3-D structural "picture" of BAF complexes purified directly from human cells in their native states --
rather than artificially synthesized in the laboratory -providing an opportunity to spatially map thousands of cancer-associated mutations
to specific locations within the complex.


==========================================================================
"A 3-D structural model, or 'picture,' of how this complex actually looks inside the nucleus of our cells has remained elusive -- until now," says Kadoch. The newly obtained model represents "the most complete picture
of the human BAF complex achieved to date," said the investigators,
reporting in the journal Cell.

These new findings "provide a critical foundation for understanding human disease-associated mutations in components of the BAF complex, which
are present in over 20% of human cancers and in several intellectual
disability and neurodevelopomental disorders," the authors said. These
insights could help scientists understand how mutations in proteins
making up the complex lead to disruption of the normal regulation of DNA
and hence the expression of genes in cells, potentially causing cancerous growth of cells to form tumors. Mutations in the BAF complex, for example,
are the sole cause of rare childhood cancers such as synovial sarcoma
and malignant rhabdoid, and contribute to common cancers such as ovarian
and lung cancers.

The BAF complex is "molecular machine," a group of proteins that remodel
the way DNA is packaged in cells. It is made up of a dozen protein
subunits specified by 29 different genes. Previous attempts to obtain a structural 3- D model of the BAF complex were based on protein molecules recombinantly engineered in the laboratory, "which were unable to recreate
the entire complex," says Kadoch. She said she and her colleagues have
been trying to solve the 3-D structure of BAF since 2014, their primary
goal being a structural model that could help them inform the impact
of the mutations and ultimately, help classify mutations based on where
they are located on the "picture" of BAF. Extracting BAF complexes from
human cells was an enormous challenge: "we devised a new way of purifying
these complexes -- it took years," she says.

BAF is one of several molecular "machines" that regulate the expression
of genes in cells by modifying chromatin, a substance composed of DNA
and protein.

Chromatin packages the long DNA strand containing genes into more
condensed units. A single cell contains hundreds of thousands of chromatin-modifying complexes, of which BAF is one type. Mutations in BAF, while they don't alter the DNA code of genes to cause cancer, disrupt
DNA topology and accessibility, leading to aberrant gene expression and
the growth of malignant tumors.

Using several powerful new analytic tools in combination, the
investigators produced a model of the BAF complex's structure both as an isolated complex and in the form BAF takes when it binds to nucleosomes -- spool-like units of chromatin around which DNA segments are wound. Binding
to nucleosomes is necessary for BAF complexes to remodel chromatin and influence gene expression.

One of the newest and most helpful tools the researchers used to
obtain the structure of BAF bound to nucleosomes is called cryo-EM,
a form of electron microscopy that can create high-resolution models
of molecules in their native environment, and which scientists say
is revolutionizing the field of structural biology. The developers of
cryo-EM won a Nobel Prize in 2017. In this case, the human BAF complexes
were too heterogeneous and flexible for the method to alone produce
a high-resolution structure, but when paired with two other methods,
known as cross-linking mass-spectrometry and homology modeling, the
structural connectivity between the subunits became clearer.

Kadoch and her colleagues report that the BAF complex is made up of three modules which form a "C" shape and grip the nucleosome on opposite sides
like a carpenter's C-clamp holds pieces of wood together. They discovered
that the two regions of the BAF structure that grip the nucleosome
are "hot spots" where cancer-causing mutations frequently occur and
used experiments to show how mutations disrupt the normal regulation
of chromatin by BAF complexes. The group also found other locations
within the complex as to where known cancer mutations, contained in a
database known as COSMIC (the Catalogue of Somatic Mutations in Cancer), structurally "cluster" and resolved their functions.

"Mapping such mutations on the structure of the BAF complex and
understanding their functional impact has remained a major, unmet goal of
the field at-large for decades," said Kadoch. "This marks the beginning
of an era in which we will be able to functionally "group" mutations
that define specific tumor features and inform therapeutic opportunities."

========================================================================== Story Source: Materials provided by Dana-Farber_Cancer_Institute. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Nazar Mashtalir, Hiroshi Suzuki, Daniel P. Farrell, Akshay Sankar,
Jie
Luo, Martin Filipovski, Andrew R. D'Avino, Roodolph St. Pierre,
Alfredo M. Valencia, Takashi Onikubo, Robert G. Roeder, Yan
Han, Yuan He, Jeffrey A. Ranish, Frank DiMaio, Thomas Walz,
Cigall Kadoch. A Structural Model of the Endogenous Human
BAF Complex Informs Disease Mechanisms. Cell, 2020; DOI:
10.1016/j.cell.2020.09.051 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/10/201013111309.htm

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